parabricks/applybqsr version updated and tests migrated to nf-test #16904
Triggered via pull request
November 7, 2024 12:29
mashehu
Status
Cancelled
Total duration
16m 32s
Artifacts
–
test.yml
on: pull_request
Matrix: nf-test
Matrix: nf-test with GPUs
Matrix: nf-core-lint-modules
Matrix: nf-core-lint-modules
Matrix: pytest
confirm-pass
0s
Annotations
18 errors and 5 warnings
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nf-test with GPUs (modules/nf-core/parabricks/fq2bam, docker_self_hosted)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/parabricks/applybqsr, docker_self_hosted)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/parabricks/applybqsr, singularity)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/parabricks/fq2bam, singularity)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/parabricks/fq2bammeth)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, docker_self_hosted)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, docker_self_hosted)
The operation was canceled.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, singularity)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, singularity)
The operation was canceled.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, conda)
The run was canceled by @mashehu.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, conda)
The operation was canceled.
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nf-test (modules/nf-core/metamdbg/asm, singularity)
The run was canceled by @mashehu.
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nf-test (modules/nf-core/metamdbg/asm, singularity)
The operation was canceled.
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nf-test (modules/nf-core/metamdbg/asm, docker_self_hosted)
The run was canceled by @mashehu.
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nf-test (modules/nf-core/metamdbg/asm, docker_self_hosted)
The operation was canceled.
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nf-test (modules/nf-core/metamdbg/asm, docker_self_hosted)
Process completed with exit code 1.
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nf-test (modules/nf-core/metamdbg/asm, conda)
The run was canceled by @mashehu.
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nf-test (modules/nf-core/metamdbg/asm, conda)
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pytest-changes
The following actions use a deprecated Node.js version and will be forced to run on node20: mirpedrol/paths-filter@main. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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pre-commit
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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nf-test with GPUs (modules/nf-core/metamdbg/asm, conda)
/home/ubuntu/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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nf-test (modules/nf-core/metamdbg/asm, conda)
/home/ubuntu/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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nf-test (modules/nf-core/metamdbg/asm, conda)
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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